Last updated: 2024-03-21

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Knit directory: mi_spatialomics/

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Ignored files:
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    Ignored:    analysis/.DS_Store
    Ignored:    analysis/deprecated/.DS_Store
    Ignored:    analysis/molecular_cartography_python/.DS_Store
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    Ignored:    analysis/seqIF_python/pixie/.DS_Store
    Ignored:    analysis/seqIF_python/pixie/cell_clustering/
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    Ignored:    annotations/molkart/.DS_Store
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    Ignored:    annotations/molkart/Supplementary_Figure4_regions/.DS_Store
    Ignored:    data/.DS_Store
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    Ignored:    data/Calcagno2022_int_logNorm_annot.h5Seurat
    Ignored:    data/IC_03_IF_CCR2_CD68 cell numbers.xlsx
    Ignored:    data/Traditional_IF_absolute_cell_counts.csv
    Ignored:    data/Traditional_IF_relative_cell_counts.csv
    Ignored:    data/pixie.cell_table_size_normalized_cell_labels.csv
    Ignored:    data/results_cts_100.sqm
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    Ignored:    data/seurat/
    Ignored:    output/.DS_Store
    Ignored:    output/mol_cart.harmony_object.h5Seurat
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Untracked files:
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Unstaged changes:
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    Deleted:    figures/Supplementary_Figure_1_Molecular_Cartography_ROIs.png
    Deleted:    figures/Supplementary_figure_5.segmentation_metrics.poster.eps
    Modified:   figures/Supplementary_figure_X.proteomics.eps
    Modified:   figures/Supplementary_figure_X.proteomics.png
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File Version Author Date Message
Rmd 56559c7 FloWuenne 2024-03-21 Cleaned up repository.
Rmd 82f107f FloWuenne 2024-01-21 Updates to Molkart analysis.
Rmd f4d5c82 FloWuenne 2024-01-15 Latest update to Seurat analysis with reprocessed data.
html d40c16e FloWuenne 2024-01-15 Build site.
Rmd 51d8b3b FloWuenne 2024-01-15 wflow_publish("./analysis/data_analysis.Rmd")
Rmd 2d9b909 FloWuenne 2024-01-09 Pushing latest changes. Updating molkart data.
html 2d9b909 FloWuenne 2024-01-09 Pushing latest changes. Updating molkart data.
html 2dcd178 FloWuenne 2023-12-06 wflow_publish("*")
Rmd 5dee03d FloWuenne 2023-09-04 Latest code update.
html 5dee03d FloWuenne 2023-09-04 Latest code update.
html d7ea71e FloWuenne 2023-08-11 Build site.
Rmd 64318a3 FloWuenne 2023-08-11 wflow_publish(c("analysis/molkart.process_quantifications_seurat.Rmd",
Rmd 9b98d64 FloWuenne 2023-08-04 Updated python and R scripts for Molkart.
html 67e546d FloWuenne 2023-07-23 Build site.
Rmd ed31d81 FloWuenne 2023-07-02 Finalized proteomics analysis.
html ed31d81 FloWuenne 2023-07-02 Finalized proteomics analysis.
html c1395e6 FloWuenne 2023-06-20 Build site.
Rmd 236130c FloWuenne 2023-06-20 Updating proteomic analysis.
html 236130c FloWuenne 2023-06-20 Updating proteomic analysis.
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Rmd 0eba381 FloWuenne 2023-06-14 Updating Data analysis links.
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Rmd 2d015dd FloWuenne 2023-06-14 Finalized imputation with RF.
html 2d015dd FloWuenne 2023-06-14 Finalized imputation with RF.
html 5816aca FloWuenne 2023-06-12 Build site.
Rmd 3b5ca40 FloWuenne 2023-06-12 Added code for supplementary Figures.
html 3b5ca40 FloWuenne 2023-06-12 Added code for supplementary Figures.
html e3bbd70 FloWuenne 2023-06-12 Build site.
Rmd 412d64f FloWuenne 2023-06-12 Fixed links in data_analysis
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Rmd ff0c849 FloWuenne 2023-06-12 wflow_publish("*")
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Rmd ebb85a5 FloWuenne 2023-06-12 Updated organization for proteomics data analysis.
html 51754b9 FloWuenne 2023-06-12 Build site.
html d764fa8 FloWuenne 2023-06-12 Build site.
Rmd 62020bf FloWuenne 2023-06-12 Configure site header.

Molecular Cartography

These scripts were used to analyze Molecular Cartography data following processing with the nf-Molkart pipeline.